Defining the Protein Complex Proteome of Plant Mitochondria

Overview

Journal Plant Physiol

Specialty Physiology

Date 2011 Aug 16

PMID 21841088

Citations 82

Authors

Jennifer Klodmann

Michael Senkler

Christina Rode

Hans-Peter Braun

Affiliations

Soon will be listed here.

Abstract

A classical approach, protein separation by two-dimensional blue native/sodium dodecyl sulfate-polyacrylamide gel electrophoresis, was combined with tandem mass spectrometry and up-to-date computer technology to characterize the mitochondrial "protein complex proteome" of Arabidopsis (Arabidopsis thaliana) in so far unrivaled depth. We further developed the novel GelMap software package to annotate and evaluate two-dimensional blue native/sodium dodecyl sulfate gels. The software allows (1) annotation of proteins according to functional and structural correlations (e.g. subunits of a distinct protein complex), (2) assignment of comprehensive protein identification lists to individual gel spots, and thereby (3) selective display of protein complexes of low abundance. In total, 471 distinct proteins were identified by mass spectrometry, several of which form part of at least 35 different mitochondrial protein complexes. To our knowledge, numerous protein complexes were described for the first time (e.g. complexes including pentatricopeptide repeat proteins involved in nucleic acid metabolism). Discovery of further protein complexes within our data set is open to everybody via the public GelMap portal at www.gelmap.de/arabidopsis_mito.

Citing Articles

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References

Heazlewood J, Tonti-Filippini J, Verboom R, Millar A . Combining experimental and predicted datasets for determination of the subcellular location of proteins in Arabidopsis. Plant Physiol. 2005; 139(2):598-609. PMC: 1255979. DOI: 10.1104/pp.105.065532. View

Peters K, Dudkina N, Jansch L, Braun H, Boekema E . A structural investigation of complex I and I+III2 supercomplex from Zea mays at 11-13 A resolution: assignment of the carbonic anhydrase domain and evidence for structural heterogeneity within complex I. Biochim Biophys Acta. 2007; 1777(1):84-93. DOI: 10.1016/j.bbabio.2007.10.012. View

Neuhoff V, Arold N, Taube D, Ehrhardt W . Improved staining of proteins in polyacrylamide gels including isoelectric focusing gels with clear background at nanogram sensitivity using Coomassie Brilliant Blue G-250 and R-250. Electrophoresis. 1988; 9(6):255-62. DOI: 10.1002/elps.1150090603. View

Schagger H, von Jagow G . Blue native electrophoresis for isolation of membrane protein complexes in enzymatically active form. Anal Biochem. 1991; 199(2):223-31. DOI: 10.1016/0003-2697(91)90094-a. View

Klodmann J, Braun H . Proteomic approach to characterize mitochondrial complex I from plants. Phytochemistry. 2010; 72(10):1071-80. DOI: 10.1016/j.phytochem.2010.11.012. View

Meyer E, Taylor N, Millar A . Resolving and identifying protein components of plant mitochondrial respiratory complexes using three dimensions of gel electrophoresis. J Proteome Res. 2008; 7(2):786-94. DOI: 10.1021/pr700595p. View

Heinemeyer J, Scheibe B, Schmitz U, Braun H . Blue native DIGE as a tool for comparative analyses of protein complexes. J Proteomics. 2009; 72(3):539-44. DOI: 10.1016/j.jprot.2008.12.008. View

Jenner H, Winning B, Millar A, Tomlinson K, Leaver C, Hill S . NAD malic enzyme and the control of carbohydrate metabolism in potato tubers. Plant Physiol. 2001; 126(3):1139-49. PMC: 116470. DOI: 10.1104/pp.126.3.1139. View

Heazlewood J, Howell K, Whelan J, Millar A . Towards an analysis of the rice mitochondrial proteome. Plant Physiol. 2003; 132(1):230-42. PMC: 166968. DOI: 10.1104/pp.102.018986. View

10.

Werhahn W, Braun H . Biochemical dissection of the mitochondrial proteome from Arabidopsis thaliana by three-dimensional gel electrophoresis. Electrophoresis. 2002; 23(4):640-6. DOI: 10.1002/1522-2683(200202)23:4<640::AID-ELPS640>3.0.CO;2-F. View

11.

Lee C, Eubel H, OToole N, Millar A . Combining proteomics of root and shoot mitochondria and transcript analysis to define constitutive and variable components in plant mitochondria. Phytochemistry. 2011; 72(10):1092-108. DOI: 10.1016/j.phytochem.2010.12.004. View

12.

Eubel H, Jansch L, Braun H . New insights into the respiratory chain of plant mitochondria. Supercomplexes and a unique composition of complex II. Plant Physiol. 2003; 133(1):274-86. PMC: 196604. DOI: 10.1104/pp.103.024620. View

13.

Lister R, Hulett J, Lithgow T, Whelan J . Protein import into mitochondria: origins and functions today (review). Mol Membr Biol. 2005; 22(1-2):87-100. DOI: 10.1080/09687860500041247. View

14.

Kruft V, Eubel H, Jansch L, Werhahn W, Braun H . Proteomic approach to identify novel mitochondrial proteins in Arabidopsis. Plant Physiol. 2001; 127(4):1694-710. PMC: 133574. View

15.

Klodmann J, Sunderhaus S, Nimtz M, Jansch L, Braun H . Internal architecture of mitochondrial complex I from Arabidopsis thaliana. Plant Cell. 2010; 22(3):797-810. PMC: 2861459. DOI: 10.1105/tpc.109.073726. View

16.

Zhou Z, McCARTHY D, OConnor C, Reed L, STOOPS J . The remarkable structural and functional organization of the eukaryotic pyruvate dehydrogenase complexes. Proc Natl Acad Sci U S A. 2001; 98(26):14802-7. PMC: 64939. DOI: 10.1073/pnas.011597698. View

17.

Mozo T, Fischer K, Flugge U, Schmitz U . The N-terminal extension of the ADP/ATP translocator is not involved in targeting to plant mitochondria in vivo. Plant J. 1995; 7(6):1015-20. DOI: 10.1046/j.1365-313x.1995.07061015.x. View

18.

Emmermann M, Braun H, Schmitz U . The ADP/ATP translocator from potato has a long amino-terminal extension. Curr Genet. 1991; 20(5):405-10. DOI: 10.1007/BF00317069. View

19.

Rode C, Senkler M, Klodmann J, Winkelmann T, Braun H . GelMap-a novel software tool for building and presenting proteome reference maps. J Proteomics. 2011; 74(10):2214-9. DOI: 10.1016/j.jprot.2011.06.017. View

20.

Heazlewood J, Howell K, Millar A . Mitochondrial complex I from Arabidopsis and rice: orthologs of mammalian and fungal components coupled with plant-specific subunits. Biochim Biophys Acta. 2003; 1604(3):159-69. DOI: 10.1016/s0005-2728(03)00045-8. View